chr11-102347161-G-C

Variant names:

• chr11-102347161-G-C
• rs1318199
• ENST00000687499.3:n.449C>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000687499.3(ENSG00000288833):​n.449C>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0437 in 152,308 control chromosomes in the GnomAD database, including 198 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.044 (198 hom., cov: 35)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: ENSG00000288833 ENST00000687499.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0310
• Publications: 3 publications found

Genes affected

ENSG00000288833 (HGNC:):

BIRC2 (HGNC:590): (baculoviral IAP repeat containing 2) The protein encoded by this gene is a member of a family of proteins that inhibits apoptosis by binding to tumor necrosis factor receptor-associated factors TRAF1 and TRAF2, probably by interfering with activation of ICE-like proteases. This encoded protein inhibits apoptosis induced by serum deprivation and menadione, a potent inducer of free radicals. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jan 2012]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.72).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0677 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BIRC2	NM_001166.5	c.-1473G>C		upstream_gene_variant		ENST00000227758.7	NP_001157.1
BIRC2	NM_001256163.1	c.-1942G>C		upstream_gene_variant			NP_001243092.1
BIRC2	NM_001256166.2	c.-217G>C		upstream_gene_variant			NP_001243095.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BIRC2	ENST00000227758.7	c.-1473G>C		upstream_gene_variant		1	NM_001166.5	ENSP00000227758.2

Frequencies

GnomAD3 genomes AF: 0.0438 AC: 6660 AN: 152190 Hom.: 198 Cov.: 35

Gnomad AFR AF: 0.0143

Gnomad AMI AF: 0.0921

Gnomad AMR AF: 0.0375

Gnomad ASJ AF: 0.0689

Gnomad EAS AF: 0.00540

Gnomad SAS AF: 0.0174

Gnomad FIN AF: 0.0231

Gnomad MID AF: 0.0318

Gnomad NFE AF: 0.0693

Gnomad OTH AF: 0.0425

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 28 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 22

African (AFR) AC: 0 AN: 0

American (AMR) AF: 0.00 AC: 0 AN: 2

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 0.00 AC: 0 AN: 2

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 24

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.0437 AC: 6661 AN: 152308 Hom.: 198 Cov.: 35 AF XY: 0.0407 AC XY: 3035 AN XY: 74490

African (AFR) AF: 0.0143 AC: 594 AN: 41580

American (AMR) AF: 0.0375 AC: 574 AN: 15308

Ashkenazi Jewish (ASJ) AF: 0.0689 AC: 239 AN: 3468

East Asian (EAS) AF: 0.00560 AC: 29 AN: 5176

South Asian (SAS) AF: 0.0174 AC: 84 AN: 4832

European-Finnish (FIN) AF: 0.0231 AC: 245 AN: 10620

Middle Eastern (MID) AF: 0.0308 AC: 9 AN: 292

European-Non Finnish (NFE) AF: 0.0693 AC: 4714 AN: 68004

Other (OTH) AF: 0.0421 AC: 89 AN: 2116

Alfa AF: 0.0596 Hom.: 45

Bravo AF: 0.0429

Asia WGS AF: 0.0140 AC: 50 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
CADD	Benign	7.3
DANN	Benign	0.75
PhyloP100		0.031
PromoterAI		0.14	Neutral

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs1318199; hg19: chr11-102217892;